Bash Script To Bp_Fetch A List Of Cds Acession Numbers

Question

[eddie.im]

Hello,

I'm trying to write a bash script to use bioperl bash command bp_fetch and return a CDS list in fasta format.

I have installed bioperl and bp_fetch works as intended:

xxxx@xxxx:~/Documents$ bp_fetch net::embl:AAA24658.1

>AAA24658 Escherichia coli hypothetical protein
ATGGAACGTTGCGGCTGGGTGAGTCAGGACCCGCTTTATATTGCCTACCATGATAATGAG
TGGGGCGTGCCTGAAACTGACAGTAAAAAACTGTTCGAAATGATCTGCCTTGAAGGGCAG
CAGGCTGGATTATCGTGGATCACCGTCCTCAAAAAACGCGAAAACTATCGCGCCTGCTTT
CATCAGTTCGATCCGGTGAAGGTCGCAGCAATGCAGGAAGAGGATGTCGAAAGACTGGTA
CAGGACGCCGGGATTATCCGCCATCGAGGGAAAATTCAGGCAATTATTGGTAATGCGCGG
GCGTACCTGCAAATGGAACAGAACGGCGAACCGTTTGTCGACTTTGTCTGGTCGTTTGTA
AATCATCAGCCACAGGTGACACAAGCCACAACGTTGAGCGAAATTCCCACATCTACGTCC
GCCTCCGACGCCCTATCTAAGGCACTGAAAAAACGTGGTTTTAAGTTTGTCGGCACCACA
ATCTGTTACTCCTTTATGCAGGCATGTGGGCTGGTGAATGATCATGTGGTTGGCTGCTGT
TGCTATCCGGGAAATAAACCATGA

The problem is that i have a file with long list of acession numbers, and i'm trying to do a bash script to run "bp_fetch net::" with every line of the file (each line has an acession number) and output the list of FASTA CDS's in a txt file. I have tried something like:

for line in $file
do
    bp_fetch net::$line

But I'm having no success. Can I get some help?

Thanks in advance.

Answer 1

[Frédéric Mahé]

You can try something like that (assuming the accessions are listed in the file accessions.list):

while read accession_number ; do bp_fetch net::${accession_number} ; done < accessions.list > results.txt

Note that you can inject the list of accessions at the end of the while loop (< accessions.list), and collect the results in a new file (> results.txt).

[eddie.im]

Hey Frédéric, thanks a lot! Your script worked flawlessly! :)

Answer 2

[lh3]

cat accessions.list | xargs -i echo bp_fetch net::{} | sh > results.txt

I use the above command line more often as I can check whether the command line is correct before feeding is to sh. The shorter version is:

xargs -i bp_fetch net::{} < accessions.list > results.txt

I believe you can also give bp_fetch multiple accessions in the command line. In that case:

cat accessions.list | sed s,^,net::, | xargs bp_fetch > results.txt